Yes, I’ve had similar issues (and for the same reasons I’ve switched to outputting to an MKV container using Handbrake).

I’ve also been able to repair my MP4 files by using mkvmerge and repackaging them in an MKV container (and also checking AAC sound on the sound track in the track specific options). This is a good alternative to re-encoding (since it’s lightning fast) but, of course, doesn’t help if you need to keep the MP4 file (unless you want to keep two separate copies in different containers).

WD has certainly heard of enough issues with MP4 files – whether they are actively working on fixing them I don’t know (but I can find out).

There are a lot of great freeware tools out there – I’d also add txMuxer into the mix (so to speak :>) and, for sub title work, BDSup2Sub. And without such behind the scenes tools as ffmpeg we’d be in big trouble. While it’s unfortunate that the Live can’t handle all file types, at least there are ways of handling almost any file problem we encounter.